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Full Discussion: A find and replace script
Operating Systems Linux A find and replace script Post 302659943 by herasj01 on Thursday 21st of June 2012 04:49:03 PM
Old 06-21-2012
A find and replace script

Hello everyone,
I am trying to do a simple script (shell or perl) for a bioinformatic problem, where I want to use a list from file2 and append this information to file1 (output).

Example:
File1
Code:
>Apple1 
GAGACGATTTATATATAGAAGAGAG
>Banana2 
CAGAGAGAGAGACCCCCCCCCCCC

File2
Code:
>Apple1      20     100
>Banana2    30     300

Ouput (new File1)
Code:
>Apple1   20     100
GAGACGATTTATATATAGAAGAGAG
>Banana2  30     300
CAGAGAGAGAGACCCCCCCCCCCC


If anyone has any feedback that would be greatly appreciated.


Cheers

herasj

Last edited by Scrutinizer; 06-21-2012 at 05:49 PM.. Reason: code tags
 

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DIFF3(1)						      General Commands Manual							  DIFF3(1)

NAME
diff3 - 3-way differential file comparison SYNOPSIS
diff3 [ -exEX3 ] file1 file2 file3 DESCRIPTION
Diff3 compares three versions of a file, and publishes disagreeing ranges of text flagged with these codes: ==== all three files differ ====1 file1 is different ====2 file2 is different ====3 file3 is different The type of change suffered in converting a given range of a given file to some other is indicated in one of these ways: f : n1 a Text is to be appended after line number n1 in file f, where f = 1, 2, or 3. f : n1 , n2 c Text is to be changed in the range line n1 to line n2. If n1 = n2, the range may be abbreviated to n1. The original contents of the range follows immediately after a c indication. When the contents of two files are identical, the contents of the lower-numbered file is suppressed. Under the -e option, diff3 publishes a script for the editor ed that will incorporate into file1 all changes between file2 and file3, i.e. the changes that normally would be flagged ==== and ====3. Option -x (-3) produces a script to incorporate only changes flagged ==== (====3). The following command will apply the resulting script to `file1'. (cat script; echo '1,$p') | ed - file1 The -E and -X are similar to -e and -x, respectively, but treat overlapping changes (i.e., changes that would be flagged with ==== in the normal listing) differently. The overlapping lines from both files will be inserted by the edit script, bracketed by "<<<<<<" and ">>>>>>" lines. For example, suppose lines 7-8 are changed in both file1 and file2. Applying the edit script generated by the command "diff3 -E file1 file2 file3" to file1 results in the file: lines 1-6 of file1 <<<<<<< file1 lines 7-8 of file1 ======= lines 7-8 of file3 >>>>>>> file3 rest of file1 The -E option is used by RCS merge(1) to insure that overlapping changes in the merged files are preserved and brought to someone's atten- tion. FILES
/tmp/d3????? /usr/libexec/diff3 SEE ALSO
diff(1) BUGS
Text lines that consist of a single `.' will defeat -e. 7th Edition October 21, 1996 DIFF3(1)
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